FBIAgentJohn Doggett arrives at the Blackstone XL pipeline in Crook County, Wyoming with a few colleagues to investigate a potential threat to the pipeline. A crowd of protesters has gathered at the site. Doggett questions a work supervisor to determine if he has noticed anything unusual. The man says he hasn't, except for the protesters. As Doggett walks along the pipeline, the metal chain attached to his badge is strongly attracted by a magnetic force inside the pipe. Doggett enters the pipeline and finds a flow of glittering liquid instead of crude oil. The supervisor, standing behind him, shape-shifts into a cloaked figure and attacks the agent. A violent explosion occurs soon after.

Spotsylvania County, Virginia10:02 A.M.

Fox Mulder and Walter Skinner make their way to the Associated Medical Professionals clinic where Dana Scully was last seen. A trail of bloodstains leads them to the end of a back alley. Skinner mentions Scully had recently ordered blood work on a child named Emily Van De Kamp and both the girl and her mother have gone missing since. It also seems that all information concerning these individuals had been forged. Skinner underlines the strangeness of the fact that William's adoptive family in Wyoming was also named Van De Kamp. FBI agents have already been sent to check on the family, but nobody should have been able to find out who had adopted William but the FBI. Mulder ponders a moment, then walks away, saying he is going to get help from someone he can trust, leaving Skinner exasperated.

Half-remembering in a dream, Dana Scully sees herself giving birth to her son William, begging Monica Reyes not to let a group of onlookers take him. The group shape-shifts into the cloaked figures involved in the recent events. Scully wakes up inside a small cabin in a snowy, forested landscape. She notices her wounded arm has somehow been healed. She runs outside and is about to step out of a large alien symbol surrounding the cabin, when a voice in her head orders her to stop. Three cloaked men are standing before her. She asks who they are and what they want. As they approach menacingly, she begins to fight them. One of the men produces a dagger and, in an alien language, declares, "We have found the bringer… Through her we shall find the…", but he is interrupted when a glittering liquid is sprayed upon the trio, disintegrating their bodies immediately. Another cloaked man who is responsible for the spraying and referred to as "Deacon" walks towards Scully. The woman grabs the dagger to protect herself, but Deacon takes control of her mind and forces her to drop it, telling her they are now leaving this place. Scully believes Deacon and the other cloaked figures are like Jeremiah Smith or the Alien Bounty Hunters, and that the cloaked individuals are either super-soldier replacements or alien-human hybrids. Deacon rather uses the term "Acolytes" and replies they will continue coming until she is secured. Scully asks why they will keep doing so, a question Deacon says Scully already knows the answer to. She accuses him of being a liar as well as the cloaked figure who shot her.

Arlington National Cemetery5:38 p.m.

A group of visitors is listening to a tour guide explaining the meaning behind Arlington National Cemetery's various monuments. Mulder is standing among them, looking at a map. The back of the map has been inscribed with the words "In case of emergency, break glass," and signed "TLG." Mulder grabs a shovel from under his long trench coat.

10:17 p.m.

Night has fallen and Mulder is alone in the cemetery, digging up Melvin Frohike's grave. He has removed only a foot of dirt when he finds a door near the surface. A security guard catches Mulder in the act and calls out to him. Mulder tries to justify his actions but the guard, holding up a bright flashlight to Mulder's face, reproves him for being disrespectful to the American heroes buried there. The guard calls Mulder by name then tells him to open the door, lowering the flashlight and allowing him to see his face; the guard is none other than Frohike. A set of stairs leads to a tunnel underground, and as the men enter, Frohike explains how the Lone Gunmen faked their own deaths; since the FBI helped them while Mulder was away, they agreed to work off the debt and help troubleshoot the government's technological vulnerabilities. He goes on to say they were made aware of Mulder's involvement in this case but that it is serious business, since he is no longer an FBI agent. Mulder insists he and Scully need Frohike's help.

The tunnel leads to a high-tech office where Mulder finds Richard Langly and John Fitzgerald Byers keeping busy around the room. Mulder informs Byers about the outside entity who accessed the records of FBI personnel associated with the X-files. Mulder suspects identifying the culprit will lead them to Scully. Byers thinks she has more to do with the journey than the destination. He then mentions the incident at the Blackstone XL work site and the dispatched Agent Doggett being unaccounted for. Mulder asks the Lone Gunmen to go through adoption records using the name "Van De Kamp".

While Mulder recalls how – twelve years prior – Scully gave birth to a baby she couldn't keep because it was endangered by individuals conspiring with Alien Colonists, a confused Scully is threatening Deacon with the dagger, but her nose starts to bleed, she drops the knife and weakly asks, "How are you in my head?" before he reaches towards her. Beginning to see a pattern in the recent incidents, Mulder instructs the Gunmen to dig up everything they can on the pipeline and to pull the FBI phone records to see if anything leads back to some kind of organization, just as Deacon picks up the now-unconscious Scully and carries her into a forest through which the Blackstone XL pipeline runs.

Back at the Lone Gunmen's office, a puzzled Mulder asks how the trio found out he was coming again. A shadowy figure smoking a Morleycigarette is meanwhile taking a stroll through Arlington National Cemetery, dropping a cigarette box on the grass.